Mixtures of osmolytes are present in the cell. Therefore, the understanding of the interplay of mixed osmolyte molecules and their combined effects on protein structure is of fundamental importance. In this article, the structure stability of a model protein (BdpA) in the mixture of guanidinium thiocyanate (GdmSCN) and methanol (MeOH) was investigated by molecular dynamics simulation. It was observed that guanidinium (Gdm(+)) is driven to protein surface by favorable electrostatic interactions and MeOH is driven by both favorable electrostatic and VDW interactions, respectively. The mixture of Gdm(+) and MeOH doesnot affect the electrostatic energy distribution of Gdm(+) but does reduce the difference in VDW energy of MeOH between the regions of protein surface and bulk solution. As a result, the accumulation level of Gdm(+) is not influenced, but the accumulation level of MeOH is lowered in mixed solution. The tertiary structure stability of protein is determined by the accumulated strength of VDW interactions from MeOH to protein side chain, and the secondary structure stability is correlated to the strength of combined electrostatic energies from solvent (water) and cosolvent (Gdm(+) and MeOH) to protein backbone, particularly in hydrogen bonding part. The mixture of GdmSCN with low-concentrated MeOH stabilizes native structure of BdpA whereas the further increase of MeOH concentration denatures native structure of protein to expanded unfolded structure. The present study together with our previous study on the mixture of GdmSCN and 2,2,2-trifluoroethanol (TFE) provides novel insights into the effects of mixed osmolytes on protein structure.